To understand the adaptive evolution of endangered plateau freshwater fishes to environmental stress and to better explore the underlying mechanisms in Aspiorhynchus laticeps—a critically endangered fish endemic to the Tarim Basin, Xinjiang, China—a combination of ecological experiments and transcriptome sequencing (RNA-seq) technology was used to study the differences in gene expression patterns among individuals under different salinities and flow conditions. This experiment included four treatment groups (CON, H-SA-S, L-SA, L-SA-S). A. laticeps specimens with an average weight of 2.92 ± 0.62 g and a body length of 58.22 ± 5.10 mm were selected, with three biological replicates for a 96 h combined stress treatment. Moreover, the relationships between these differences and the aquatic environment were analyzed. A total of 1847 differentially expressed genes (DEGs), including 935 upregulated genes and 912 downregulated genes, were identified under different aquatic environment stress modes. GO and KEGG enrichment analyses revealed that TNF signal transduction, the NF-κB pathway, and metabolic regulation were significantly enriched among the DEGs (p < 0.05). High salinity–alkali stress significantly activates the TNF/NF-κB pathway, regulates MST1, LOC107702867, LOC113110979 and other genes to enhance the body’s resistance; water flow changes mainly regulate energy metabolism through genes such as NEHOM01_1600 and gptl. These findings provide an important scientific basis for the ecological adaptability, protection, and proliferation of endemic and endangered fish in China, as well as for germplasm innovation to address ecological deterioration in plateau fishes in alpine and arid areas. This study provides a molecular-level theoretical foundation for artificial habitat regulation and the conservation of endangered Aspiorhynchus laticeps populations in the Tarim River.

The intensification of human activities in recent years has led to significant overexploitation of Triplophysa strauchii populations, resulting in a decline in the species’ natural stocks. This underscores the need for research and development initiatives aimed at supporting the recovery and sustainable management of the species. Therefore, this study investigated its biological traits and isozyme characteristics in detail. First, throutigations of fish ecology, the age and growth patterns of T. strauchii were examined. The results revealed that the length of the otoliths was greater than the width and that the intermajor groove was indistinct. The age range of the fish was 0–4 years. A correlation between body length and weight revealed that T. strauchii exhibited isometric growth patterns. In terms of growth parameters, the inflection point in age for T. strauchii was t_i = 3.23. Additionally, to analyze the enzymes lactate dehydrogenase (LDH), malate dehydrogenase (MDH), and esterase (EST) in ten tissues of T. strauchii (liver, muscle, heart, gills, eye, brain, fins, kidneys, gonads, and intestines), vertical plate electrophoresis was performed via polyacrylamide gels. The results of isoenzyme analysis revealed that the LDHA (lactate dehydrogenase A subunit) gene was predominant in all tissues. A maximum of two s-MDH enzyme bands with three m-MDH enzyme bands were detected, with a classic enzyme profile and no gene mutation. The EST enzyme was highly expressed in the liver and kidney and was less polymorphic. In general, T. strauchii exhibited a spindle-like body shape and isometric growth patterns in the Turks River. It exhibited a narrow age range, strong adaptability, and stable genetic traits. This species has high development potential, utilization value and ecological significance.